getData {RIVER} | R Documentation

## Get coordinated data from a compressed file for RIVER

### Description

`getData` extracts genomic features, z-scores of gene expression, and N2 pairs having same rare variants from an imported compressed data, computes outlier status from z-scores given a z-score threshold and coordinates the genomic features, outlier status, and a list of N2 pairs into ExpressionSet class having standardized data structure.

### Usage

    getData(filename = system.file("extdata", "simulation_RIVER.gz", package =
      "RIVER"), ZscoreThrd = 1.5)

### Arguments

`filename` | A full path of a compressed input file that consists of all samples in rows and subject ID, gene name, genomic features, z-scores of corresponding gene expression, and a list of N2 pairs in columns from left to right. In N2 pairs, samples not paired with othersamples have NA while two samples sharing same rare variant near a gene have same pre-assigend integers.
`ZscoreThrd` | A |Z-score| threshold for defining outlier status of samples

### Value

dataInput An object of ExpressionSet class which contains input data required for all functions in RIVER including genomic features, outlier status, and N2 pairs.

### Author(s)

Yungil Kim, ipw012@gmail.com

### See Also

`fread`, `ExpressionSet`,

### Examples

    InputData <- getData(filename=system.file("extdata", "simulation_RIVER.gz",
            package = "RIVER"), ZscoreThrd=1.5)

[Package RIVER version 1.4.0 Index]